Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1784
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 25890
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Found at i:3894 original size:19 final size:19
Alignment explanation
Indices: 3857--3895 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
3847 TTTCTTTCGT
3857 AGATTGTTTTTGACAGTACA
1 AGATTGTTTTT-ACAGTACA
3877 AGATATGTTTTT-CAGTACA
1 AGAT-TGTTTTTACAGTACA
3896 TTTTGTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (19 bp):
AGATTGTTTTTACAGTACA
Found at i:7775 original size:13 final size:13
Alignment explanation
Indices: 7757--7782 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7747 AAATGAGTTG
7757 AGAGAAAATAATT
1 AGAGAAAATAATT
7770 AGAGAAAATAATT
1 AGAGAAAATAATT
7783 TATAAGAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
AGAGAAAATAATT
Found at i:10151 original size:13 final size:13
Alignment explanation
Indices: 10133--10157 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10123 GCCATGTAAG
10133 CAAAAATTAATAA
1 CAAAAATTAATAA
10146 CAAAAATTAATA
1 CAAAAATTAATA
10158 GGATTATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (13 bp):
CAAAAATTAATAA
Found at i:10386 original size:16 final size:16
Alignment explanation
Indices: 10365--10400 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
10355 TATTTATCTA
*
10365 TTGATATAAATATTAT
1 TTGATATAAATATAAT
10381 TTGATATAAATATAAT
1 TTGATATAAATATAAT
10397 TTGA
1 TTGA
10401 CTAATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (16 bp):
TTGATATAAATATAAT
Found at i:10608 original size:21 final size:21
Alignment explanation
Indices: 10566--10620 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
10556 TCAAACTATT
** **
10566 AAATTTAATTTTATTATTATA
1 AAATTTAATTTTACCACAATA
10587 AAATTTAATTTTACCACAATA
1 AAATTTAATTTTACCACAATA
10608 ATAA-TTAATTTTA
1 A-AATTTAATTTTA
10621 TTATGAATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATTTAATTTTACCACAATA
Found at i:10909 original size:12 final size:13
Alignment explanation
Indices: 10889--10925 Score: 58
Period size: 12 Copynumber: 2.8 Consensus size: 13
10879 ATTAAAATGT
10889 AATATAAAATAAA
1 AATATAAAATAAA
10902 AATA-AAAATAAA
1 AATATAAAATAAA
10914 AATATATAAATA
1 AATATA-AAATA
10926 TTTTAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.55
13 5 0.23
14 5 0.23
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATATAAAATAAA
Found at i:15380 original size:2 final size:2
Alignment explanation
Indices: 15373--15403 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
15363 ACTTTATGAC
*
15373 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15404 GAAAAACTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17413 original size:219 final size:218
Alignment explanation
Indices: 17078--17494 Score: 667
Period size: 220 Copynumber: 1.9 Consensus size: 218
17068 CCTTCCTTTC
* ** *
17078 TTCTCGTGATCTCTCTCTTTTCTTTCTTTCTTTCGTCATTAAATTAAAAAAAAAGTTTGTTTTCA
1 TTCTCGTGATCTCTCTCTTTTCTTTCTTTCTTTCGTAATTAAAAAAAAAAAAAAGTTTGCTTTCA
* *
17143 TTTAATTAGATGGTAATAATTTTCTTTCAAAAACGTAATAAATGCTTGAAGG-TTTTTTTTTTTT
66 TTTAATTAGATGATAATAATTTTCTTTCAAAAACGTAATAAATACTTGAAGGTTTTTTTTTTTTT
* *
17207 TTCATAAAGGAATTTTGCCAGTCAATAAACAAAGCATTTGTCTCATTATATATAAAAAATAAAAT
131 TTCATAAAGGAATTTTCCCAGTCAATAAACAAAGCATTTGGCTCATTATATATAAAAAATAAAAT
17272 CATTTGATTAGATGGTAATAATT
196 CATTTGATTAGATGGTAATAATT
* *
17295 TTCTTGTGATCTCTCTCTTTTCTTTCTTTC-TTCATTAAATTAAAAAAAAAAACAAAGTTTGCTT
1 TTCTCGTGATCTCTCTCTTTTCTTTCTTTCTTTC-GT-AATTAAAAAAAAAAA-AAAGTTTGCTT
* *
17359 TCATTTGATTAGATGATAATAATTTTCTTTCAAAAATGTAATAAATACTTGAAGGTTTTTTTTTT
63 TCATTTAATTAGATGATAATAATTTTCTTTCAAAAACGTAATAAATACTTGAAGGTTTTTTTTTT
* *
17424 TTTTTCATAAAGGGATTTTCCCAGTCAATAAACAAAGCATTTGGCTCATTATATATAAAATATAA
128 TTTTTCATAAAGGAATTTTCCCAGTCAATAAACAAAGCATTTGGCTCATTATATATAAAAAATAA
17489 AATCAT
193 AATCAT
17495 ATTAACAGGT
Statistics
Matches: 182, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
216 3 0.02
217 30 0.16
218 12 0.07
219 61 0.34
220 76 0.42
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (218 bp):
TTCTCGTGATCTCTCTCTTTTCTTTCTTTCTTTCGTAATTAAAAAAAAAAAAAAGTTTGCTTTCA
TTTAATTAGATGATAATAATTTTCTTTCAAAAACGTAATAAATACTTGAAGGTTTTTTTTTTTTT
TTCATAAAGGAATTTTCCCAGTCAATAAACAAAGCATTTGGCTCATTATATATAAAAAATAAAAT
CATTTGATTAGATGGTAATAATT
Found at i:19089 original size:8 final size:9
Alignment explanation
Indices: 19064--19123 Score: 50
Period size: 9 Copynumber: 6.2 Consensus size: 9
19054 ACATCAACTC
19064 AATAATTAA
1 AATAATTAA
19073 AATAATTAA
1 AATAATTAA
19082 AA-AATTAA
1 AATAATTAA
*
19090 TATAATAATATA
1 AATAAT--TA-A
*
19102 AATAAATAAA
1 AAT-AATTAA
19112 AATATATTAA
1 AATA-ATTAA
19122 AA
1 AA
19124 ATATAATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
8 7 0.17
9 15 0.37
10 10 0.24
11 3 0.07
12 3 0.07
13 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATTAA
Found at i:23233 original size:13 final size:13
Alignment explanation
Indices: 23215--23240 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23205 AAATGAGTTG
23215 AGAGAAAATAATT
1 AGAGAAAATAATT
23228 AGAGAAAATAATT
1 AGAGAAAATAATT
23241 TATAAGAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
AGAGAAAATAATT
Found at i:24570 original size:20 final size:22
Alignment explanation
Indices: 24545--24592 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
24535 TTCAAAACTC
**
24545 ATTCTTTTTTGATT-TT-GCAA
1 ATTCTTTACTGATTCTTCGCAA
24565 ATTCTTTACTGATTCTTCGCAA
1 ATTCTTTACTGATTCTTCGCAA
24587 ATTCTT
1 ATTCTT
24593 GTTGAATCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.50
21 2 0.08
22 10 0.42
ACGTcount: A:0.21, C:0.17, G:0.08, T:0.54
Consensus pattern (22 bp):
ATTCTTTACTGATTCTTCGCAA
Found at i:25606 original size:13 final size:13
Alignment explanation
Indices: 25588--25612 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25578 CGCATGTAAG
25588 CAAAAATTAATAA
1 CAAAAATTAATAA
25601 CAAAAATTAATA
1 CAAAAATTAATA
25613 GGATTATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (13 bp):
CAAAAATTAATAA
Done.